Peptide Calculator: Molecular Mass Calculation and More

What is a Peptide Mass Calculator?

A peptide mass calculator is a helpful tool for researchers working with peptides. It allows you to determine key molecular properties of peptides, including molecular mass, sum formula, lipophilicity (XlogP), topological polar surface area (TPSA), Van-der-Waals volume, estimated counterion count, and the exact mass of the peptide without counterions. These calculations are useful for peptide studies and bioavailability assessments.

structural formula of the peptide SIINFEKL

The data is calculated based on the Chemistry Development Kit (CDK) v2.0. We assume no responsibility for its accuracy. If you notice any errors, please contact us.

Drawing of a screen showing the structural formula of a peptide and various parameters flying out

What the Peptide Mass Calculator Provides

Our peptide mass calculator simplifies complex calculations by instantly analyzing the peptide sequence you input. Beyond molecular mass, the calculator provides additional molecular properties essential for peptide research in seconds. These are the key properties in more detail:

Molecular Mass: The precise mass of the peptide molecule in Daltons (Da).
Sum Formula: The chemical composition of the peptide, showing the number of each type of atom.
XlogP: A measure of the peptide’s hydrophobicity, important for solubility and drug design. XlogP is a computationally derived estimate of the logarithm of the partition coefficient (logP) between octanol and water, which reflects how well a molecule can dissolve in lipophilic versus hydrophilic environments.
TPSA (Topological Polar Surface Area): Indicates the polar surface area, which influences permeability and absorption. TPSA is calculated based on the sum of polar atomic contributions (such as oxygen and nitrogen) in a molecule. It helps predict a molecule’s ability to cross biological membranes, making it an important parameter in drug design and bioavailability studies.

Van-der-Waals Volume: The volume fraction of the molecule determined by Van-der-Waals forces, which is important for predicting physical properties. This parameter provides insight into molecular interactions, steric effects, and the spatial arrangement of atoms within the molecule.
Estimated Counterion Count: The approximate number of counterions associated with the molecule; important for predicting electrolyte behavior.
Peptide Mass Without Counterions: The net mass of the peptide after removing counterions.

Our Peptide Mass Calculator is the ideal tool to facilitate your peptide research and analysis!

Left part of the SIINFEKL peptide with TFA as counter ion

Van-der-Waals Volume: The volume fraction of the molecule determined by Van-der-Waals forces, which is important for predicting physical properties. This parameter provides insight into molecular interactions, steric effects, and the spatial arrangement of atoms within the molecule.
Estimated Counterion Count: The approximate number of counterions associated with the molecule; important for predicting electrolyte behavior.
Peptide Mass Without Counterions: The net mass of the peptide after removing counterions.

Our Peptide Mass Calculator is the ideal tool to facilitate your peptide research and analysis!

Understanding Molecular Mass versus Molar Mass

One common question when working with peptides is the difference between molecular mass and molar mass:

Molecular Mass refers to the mass of a single molecule of a substance, expressed in atomic mass units (Da or u). It is calculated based on the sum of the atomic masses of all atoms in the molecule.
Molar Mass is the mass of one mole (6.022 × 10²³ molecules) of a substance, expressed in grams per mole (g/mol). While molecular mass is a fixed value for each molecule, molar mass provides a macroscopic perspective for laboratory calculations.

Understanding Molecular Mass versus Molar Mass

One common question when working with peptides is the difference between molecular mass and molar mass:

Molecular Mass refers to the mass of a single molecule of a substance, expressed in atomic mass units (Da or u). It is calculated based on the sum of the atomic masses of all atoms in the molecule.
Molar Mass is the mass of one mole (6.022 × 10²³ molecules) of a substance, expressed in grams per mole (g/mol). While molecular mass is a fixed value for each molecule, molar mass provides a macroscopic perspective for laboratory calculations.